Polymethine chain modified trimethine cyanine based fluorescent probe to selectively light up G-quadruplexes DNA in mitochondria

Abstract

G-quadruplex (G4) is a noncanonical nucleic acid secondary structure that has been demonstrated to have an impact on many physiological and pathological processes. To facilitate the development of small molecule drugs targeting G4, it is critical to develop functional G4 fluorescent probes that selectively reflect the unknown physiological functions of G4 and enrich the library of G4 ligand molecules. In this study, trimethine cyanine with a p-hydroxybenzyl substituent at the α-position on the polymethine chain (α-HBCy3.5) was used as a fluorescent probe for G4. By introducing bulky benzyl substituent on the polymethine chain, α-HBCy3.5 showed excellent G4 selectivity and could identify G4s from single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) by fluorescence turn-on. Thus, red fluorescence is emitted by α-HBCy3.5 in the presence of G4s (606 nm). In addition, the ability of α-HBCy3.5 to stain DNA in mitochondria in a short time (internalization in 6 min) is expected to be developed for real-time detection and monitoring of endogenous G4 DNA in living cells.